similar to: Fwd: Extract just some fields from XML]

Hello! I am trying to get specific fields from an XML document and I am totally puzzled. I hope someone can help me. # URL URL<-"http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&id=11877539,11822933,11871444&retmode=xml&rettype=citation" # download a XML file tmp <- xmlTreeParse(URL, isURL = TRUE) tmp <- xmlRoot(tmp) Now I want to extract only

Dear all, for my diploma thesis I have to import huge XML-Files into R for statistical processing - huge means a size about 33 MB. I'm using the XML-Package version 1.9 As far as reading the complete file into R via xmlTreeParse doesn't work or is too slow, I'm trying to use xmlEventParse but I got completely stuck. I have many different type of nodes + <configuration>

Hi, Consider the following code: require(XML) xmlFile = paste( "<?xml version=\"1.0\" encoding=\"ISO-8859-1\"?>\n", "<mzXML xmlns=\"a\" xmlns:xsi=\"b\" xsi:schemaLocation=\"c\">\n", "<parentFile a=\"a\" b=\"b\" />\n",

Hello! I am crossposting this to R-help and BioC, since it is relevant to both groups. I wrote a wrapper for Entrez search utility (link for this is provided bellow), which can add some new search functionality to existing code in Bioconductor's package 'annotate'*. http://eutils.ncbi.nlm.nih.gov/entrez/query/static/esearch_help.html Entrez search utuility returns a XML document

Hello everyone, I'm trying to parse a very large XML file using SAX with the XML package (i.e., mainly the xmlEventParsing function). This function takes as an argument a list of other functions (handlers) that will be called to handle particular xml nodes. If when I use Rprof(), all the handler functions are lumped together under the <anonymous> label, and I get something like this:

Dear All, I have a question regarding best practise in setting up a XML parser within R. Because I have files with more than 100 MB and I'm only interested in some values I think a SAX-like parser using xmlEventParse() will be the best solution. Unfortunately the values I'm looking for, to construct some higher "mass spectrum", are distributed over different lines: as

Could someone provide a link or examples of parsing XML document in R? Few specific questions below: For instance I can retrieve specific nodes using this: node <- xpathApply(xml, "//" %+% xtag, xmlValue) 1) I want to be able to retrieve parent node for this node, how can I do this? getParentNode() does not seem to cut it. 2) How can I retrieve children nodes for a particular

Adds two small news items and a news item on Blackberry support --- feeds/feed.rss | 28 ++++++++++++++++++++++++++++ 1 file changed, 28 insertions(+) diff --git a/feeds/feed.rss b/feeds/feed.rss index 45d8ec1..ec230aa 100644 --- a/feeds/feed.rss +++ b/feeds/feed.rss @@ -6,12 +6,29 @@ <description>The latest news about FLAC (Free Lossless Audio Codec)</description>

I''m getting an interesting problem. I''d trying to generate an RSS document and then real it from outside of my app. Here''s what the view looks like. xml.instruct! :xml, :version=>"1.0" xml.rss(:version=>"2.0"){ xml.channel{ xml.title("mytitle") xml.link("http://www.myapp.com")

--- feeds/feed.xml | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) diff --git a/feeds/feed.xml b/feeds/feed.xml index 0d16cd9..2390cd0 100644 --- a/feeds/feed.xml +++ b/feeds/feed.xml @@ -7,6 +7,30 @@ <atom:link href="http://xiph.org/flac/feeds/feed.xml" rel="self" type="application/rss+xml" /> <item> + <title>FLAC

This patch fixes a few non-ASCII characters which were displayed wrong, adds news about Pono and adds a few artists to the links page --- comparison.html | 10 +++++----- feeds/feed.xml | 18 +++++++++++++++++- links.html | 3 +++ 3 files changed, 25 insertions(+), 6 deletions(-) diff --git a/comparison.html b/comparison.html index 8e6b74b..daa0906 100644 --- a/comparison.html +++

--- developers.html | 16 ++++++++-------- documentation.html | 4 ++-- documentation_bugs.html | 2 +- documentation_example_code.html | 2 +- documentation_tools.html | 2 +- download.html | 2 +- faq.html | 2 +- feeds/feed.rss | 31 +++++++++++++++++++++++++++++--

Hi, Tomcat was running well and suddenly stop of working. I am using tomcat5-5.5.23-0jpp.7.el5_2.1 on Centos 5.2 /etc/tomcat5/tomcat5.conf looks like as follows: JAVA_HOME="/usr/lib/jvm/java" CATALINA_HOME="/usr/share/tomcat5" JASPER_HOME="/usr/share/tomcat5" CATALINA_TMPDIR="/usr/share/tomcat5/temp"

Hi all, thanks to the people who replied to my question! I finally solved the issue by writing own handlers and using xmlEventParse - which leads to the following problem which is so odd that its probably a bug. I use several special charachter in my XML-File, e.g. umlauts or ? or ? - but no matter how I encode my XML (UTF or ISO) or I escape these characters xmlEventParse always stops

Hello everyone, I am probably not the only one having trouble with this package but here goes. I want to install XML on Ubuntu. I installed libxml2-dev and everything works out fine until I get the following: Error in reconcilePropertiesAndPrototype(name, slots, prototype, superClasses, : No definition was found for superclass "namedList" in the specification of class

I unintentionally missed to cc to r-devel. -------- Original Message -------- Subject: Re: [Rd] levels for list and data.frame Date: Tue, 21 Mar 2006 20:50:21 +0100 From: Gregor Gorjanc <gregor.gorjanc at gmail.com> Reply-To: gregor.gorjanc at gmail.com To: Martin Maechler <maechler at stat.math.ethz.ch> References: <441F2C49.8080703 at gmail.com> <17439.50351.172900.987055

I tried to build (and install) XML_3.95-0.1.tar.gz on FreeBSD 10.0-CURRENT amd64, but it stopped during the check of R_HAS_REMOVE_FINALIZERS (full log appended): ---------------------------------- R CMD INSTALL XML_3.95-0.1.tar.gz [..snip..] Checking for 1.8: -DR_HAS_REMOVE_FINALIZERS=1 -I/usr/local/include/libxml2 -I/usr/local/include Using libxml2.* checking for gzopen in -lz... gcc46

I know that I''m doing something wrong, but I can''t figure out what. I''ve looked at every wiki and tutorial I can find on feedtools but I still can''t get my rss feed working. Here''s my code. feed = FeedTools::Feed.new feed.entries << FeedTools::FeedItem.new feed.entries[0].author.name = "Charlie Bowman" feed.entries[0].title =

James, thanks for the response. I understand now my puzzle. tmp <- data.frame(y1=1:4, f1=factor(c("A", "B", "C", "D"))) tmp$y2 <- NA tmp[1:2, "y2"] <- 2 Does the job. I see that I should add a full column. In my case adding full column of NAs and then adding values, solves my problems. Thanks to all. james.holtman at convergys.com

Dear, I want to read XML documents, add child nodes to some elements and store everything back as an XML document. I've tryed the following: doc <- xmlTreeParse("file.xml") QTListNode<-xmlElementsByTagName(xmlRoot(doc)[[1]],"tagname") append.xmlNode(QTListNode[[1]],newXMLNode(name ="Norm", attrs = NULL)) saveXML(doc, file = "out.xml",